Biology subjects

Chevignon, G.

Publications and source records attributed to Chevignon, G..

6 recordsLinked to original sources

bioRxiv2026

Global diversity and dispersal routes of the Ostreid herpesvirus type 1 infecting Magallana gigas

The order Herpesvirales comprises double-stranded DNA viruses characterized by substantial genomic plasticity, including recombination, structural variation, gene gain and loss, and lineage turnover. These processes can obscure phylogenetic relationships and complicate the reconstruction of viral evolutionary histories. Within this order, Ostreid herpesvirus 1 (OsHV-1) is a major pathogen of the Pacific oyster Magallana gigas and is responsible for recurrent mortality events affecting global aquaculture. Early molecular investigations based on partial genomic regions identified several viral lineages, including the "var" and "{micro}Var" lineages, but provided limited resolution for genome-wide evolutionary inference. The subsequent availability of complete genomes revealed extensive structural variation, such as insertions, deletions, and genomic rearrangements, highlighting the high genomic plasticity of OsHV-1. Although phylogenomic analyses have estimated evolutionary rates compatible with other large double-stranded DNA viruses, current inferences remain based on geographically restricted datasets, leaving the global evolutionary dynamics of OsHV-1 within its principal host insufficiently resolved. Here, we present 275 newly sequenced OsHV-1 genomes collected from infected M. gigas oysters between 1994 and 2022 across major oyster-producing regions worldwide. Using de novo genome assembly combined with comparative genomics, population genetic analyses, and time-scaled phylogenetic reconstruction, we investigate global genomic diversity and the spatio-temporal dynamics of viral diversification. Our results reveal long-standing viral diversity in East Asia, the emergence of structurally distinct Pacific and microvariants lineages, and ongoing diversification shaped by recombination, structural genome plasticity, and anthropogenic oyster movements. By integrating three decades of whole-genome data, this study provides a phylogenomic framework for understanding the diversity, evolution, and dispersal of OsHV-1 in modern aquaculture systems.

evolutionary biology↗

bioRxiv2026

Integrating coastal microbiome observations for human, oyster and environmental protection

The Reseau dObservatoires de Microbiologie Environnementale integree (ROME) was a pilot study conducted in France from September 2020 to August 2023 aiming to establish a network of eDNA-based observatories across four estuarine ecosystems associated with oyster farming: the Bay of Veys (Normandy), the Bay of Brest (Brittany), Marennes-Oleron (Nouvelle-Aquitaine), and the Thau Lagoon (Occitania). Within a One Health framework, the study assessed the influence of river inputs on estuarine microbiome structuring and the emergence of microbiological hazards affecting human, aquaculture, and ecosystem health. Over 2,000 samples were collected during the study, including biweekly surface water and monthly adult oyster samples. Environmental nucleic acids were analysed using metabarcoding (bacterial and protist communities) and metagenomics (human RNA viruses). The coastal microbiome, including pathogenic and harmful taxa relevant to humans and aquatic invertebrates, was characterized. River influence on microbial community composition was examined through spatial comparisons of stations exposed to varying levels of freshwater runoff, while oysters acted as bio-integrators of local microbial diversity. Results revealed coherent coastal-to-offshore microbiome structuring across all ecosystems, with local variations linked to riverine inputs. eDNA metabarcoding allowed to detect a wide range of prokaryotic and eukaryotic pathogens, as well as harmful algal bloom (HAB) genera, several not captured by conventional monitoring. These findings demonstrate the potential of the ROME eDNA observatory network for high-resolution, integrative surveillance of microbial biodiversity and early detection of biological risks in estuarine environments.

genomics↗

bioRxiv2025

Dynamic of the transcriptomic landscape of OsHV-1 replication in haemocytes of Pacific oyster

Since the 1990s, the Pacific oyster (Magallana gigas) has experienced repeated mortality events associated with Ostreid herpesvirus 1 (OsHV-1). Although the virus has been genomically characterised, its replication cycle and its interactions with the oyster immune system are still not well understood. In particular, little is known about the dynamics of OsHV-1 gene expression and the immune responses of haemocytes from oysters with varying susceptibility to the virus. While some studies have focused on the expression of specific viral and host genes on whole oysters, none have provided a comprehensive analysis of genomes-wide expression across multiple post-infection time points in haemocytes. The lack of oyster cell lines makes studying virus-host interactions in vitro challenging. However, haemocytes, the key immune cells circulating in hemolymph, can be maintained in vitro in the short term and represent a relevant model for analyzing infection dynamics. In this study, haemocytes from two M. gigas families, one highly susceptible and one less susceptible to OsHV-1, were infected in vitro. We tracked the viral and host transcriptomes over a 24-hour period post-infection using high-throughput dual transcriptomics. Our results provide a detailed overview of the OsHV-1 transcriptomic landscape in haemocytes from high and low susceptible M. gigas over time. In addition, WGCNA analysis of host genes expression provided insights into the haemocytes response to infection, and highlighted family-specific immune responses. This comprehensive transcriptomic study is the first to describe virus-host interactions across multiple stages of infection in haemocytes from Pacific oysters showing contrasted survival when exposed to OsHV-1. IMPORTANCEThis study provides valuable insights into the interaction between M. gigas and OsHV-1 by analyzing viral expression and host immune response at the cellular level. By focusing on haemocytes, the key immune cells in Pacific oysters, the results reveal a link between host genotype and viral transcriptomic activity, providing new perspectives on molecular basis of natural susceptibility levels to OsHV-1 infection depending of the genetic background. Overall, our findings deepen the understanding of OsHV-1 gene expression dynamics and antiviral defense mechanisms in key species cultivated worldwide.

bioinformatics↗

bioRxiv2025

Experimentally mimicking 30 years of Magallana gigas infections with the OsHV-1 virus reveals evolution through positive selection

Ostreid herpesvirus 1 (OsHV-1) poses a significant threat to the global oyster farming industry, causing substantial economic losses due to mortality outbreaks. While OsHV-1 primarily affects the Pacific oyster Magallana gigas, it has also been associated with mortality events in various other host species. Despite progress in understanding OsHV-1 epidemiology, important knowledge gaps remain regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study uses experimental evolution and extensive genomic analysis to investigate the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, play a key role in shaping viral populations, contributing to a trend toward genetic homogenization. Notably, stronger positive selection signals were observed in viral genomes isolated from oyster populations with higher susceptibility, suggesting adaptation of viral genotypes to specific host genetic backgrounds. These findings shed light on the complex evolutionary dynamics of OsHV-1 and its interactions with oyster hosts. Understanding how this virus adapts to host genetic diversity is crucial for developing strategies to mitigate its impact on the oyster farming industry and provides valuable insights into the broader mechanisms of viral evolution in response to host variation.

evolutionary biology↗

bioRxiv2024

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues

2Since the 1990s, the Pacific oyster Magallana gigas has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HWM methods and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas- infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole genome and "adaptive sampling" (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce accurate OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues. 3 ImportanceMany aquatic viruses threaten commercially valuable species and cause significant economic losses during outbreaks. To improve our understanding of the origin, transmission patterns and spread of these viruses, additional genomic data are essential. However, genomic characterization of unculturable large DNA viruses is a major challenge. In the present study, we have successfully evaluated the ability of ONT sequencing and adaptive sequencing (AS) to sequence and assemble the complete OsHV-1 genome. Our results show that it is now possible to sequence the whole genome of large DNA viruses directly from infected host tissue, without the need for prior in vitro propagation or prior laboratory steps for virus enrichment.

genomics↗

bioRxiv2023

Genetic differentiation and host specialization among OsHV-1 infecting two oyster species in France

AbstractCross-species transmission is a major driver of disease emergence in humans and animals. The Ostreavirus ostreidmalaco1 (OsHV-1) is mainly associated with mortality in the Pacific oyster Magallana gigas, but has also been found in other mollusks, including the European flat oyster Ostrea edulis. This raises questions about OsHV-1 host specificity. This study explored the genetic differentiation of OsHV-1 in M. gigas and O. edulis and the underlying mechanisms. Using high-throughput sequencing, 40 OsHV-1 genomes were obtained from both O. edulis and M. gigas and were analyzed to assess viral diversity, lineage isolation, and cross-species transmission. Comparative genomics, population genetics, phylogenetic and phylodynamic methods revealed that host species significantly influence viral genetic structure. The data suggest that OsHV-1 was introduced in Europe with M. gigas, followed by a cross-species transmission event and divergence into two distinct lineages. Selection signals were identified in genomic regions involved in key viral functions, including host binding, DNA replication, and membrane-associated proteins, indicating possible adaptation to different hosts. Future research should investigate coevolution between OsHV-1 and a broader range of host species using phylogenetic approaches to better understand host-virus dynamics.

evolutionary biology↗